SMTL ID : 6hsn.1

Crystal structure of the ternary complex of GephE-ADP-GABA(A) receptor derived peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-4-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 26 residues within 4Å: Chain A: S.188, T.189, E.192, L.193, I.205, R.206, D.207, S.208, N.209, R.210, S.254, G.255, G.256, V.257, S.258, D.263, P.289, P.308, G.309, N.310, P.311 Chain D: T.96, G.97, R.141 Ligands: MG.2, MG.3 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:S.188, A:E.192, A:E.192, A:D.207, A:S.208, A:N.209, A:G.256, A:V.257, A:S.258, A:S.258, A:S.258, A:G.309 Water bridges: A:N.209, A:N.209, A:S.258, A:S.258, A:S.258, A:N.310, D:T.96, D:R.141, D:R.141, D:R.141 ADP.18: 26 residues within 4Å: Chain A: T.96, G.97, R.141 Chain D: S.188, T.189, E.192, L.193, I.205, R.206, D.207, S.208, N.209, R.210, S.254, G.255, G.256, V.257, S.258, D.263, P.289, P.308, G.309, N.310, P.311 Ligands: MG.19, MG.20 22 PLIP interactions: 18 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:S.188, D:E.192, D:D.207, D:D.207, D:S.208, D:N.209, D:G.256, D:V.257, D:S.258, D:S.258, D:S.258, D:G.309 Water bridges: D:N.209, D:N.209, D:S.258, D:S.258, D:S.258, D:N.310, A:T.96, A:R.141, A:R.141, A:R.141

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.190, E.192, G.256 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: S.258, G.260, D.263 Ligands: ADP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.263, A:D.263, H2O.11, H2O.28 MG.19: 4 residues within 4Å: Chain D: G.190, E.192, G.256 Ligands: ADP.18 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain D: S.258, G.260, D.263 Ligands: ADP.18 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.263, D:D.263, H2O.10, H2O.29

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 13 residues within 4Å: Chain A: S.208, T.212, P.311, V.312, V.315, R.358 Chain D: L.48, I.147, S.163, G.166, L.167, T.170 Ligands: ACT.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.212, A:P.311, A:V.315 Hydrogen bonds: A:R.358, A:R.358 Water bridges: A:S.208 MPD.5: 13 residues within 4Å: Chain A: I.360, L.361, R.387, N.390, R.418, L.419 Chain D: H.159, R.327, I.332, D.334, T.338 Ligands: MPD.6, ACT.12 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:H.159, A:R.387, A:R.387 Water bridges: D:R.327, A:N.390 MPD.6: 13 residues within 4Å: Chain A: R.418, L.419 Chain D: H.159, H.220, V.323, R.327, P.337, V.415, I.416, R.418 Ligands: MPD.5, ACT.12, ACT.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.327 MPD.21: 13 residues within 4Å: Chain A: L.48, I.147, S.163, G.166, L.167, T.170 Chain D: S.208, T.212, P.311, V.312, V.315, R.358 Ligands: ACT.24 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:T.212, D:P.311, D:V.315 Hydrogen bonds: D:R.358, D:R.358 Water bridges: D:S.208 MPD.22: 13 residues within 4Å: Chain A: H.159, R.327, I.332, D.334, T.338 Chain D: I.360, L.361, R.387, N.390, R.418, L.419 Ligands: MPD.23, ACT.29 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:H.159, D:R.387, D:R.387 Water bridges: A:R.327, D:N.390 MPD.23: 13 residues within 4Å: Chain A: H.159, H.220, V.323, R.327, P.337, V.415, I.416, R.418 Chain D: R.418, L.419 Ligands: MPD.22, ACT.29, ACT.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.327

16 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 7 residues within 4Å: Chain A: N.310, P.311, V.312 Chain D: L.48, R.141, D.146 Ligands: MPD.4 Ligand excluded by PLIP ACT.8: 5 residues within 4Å: Chain A: M.19, T.20, P.21, V.22, R.301 Ligand excluded by PLIP ACT.9: 4 residues within 4Å: Chain A: T.25, A.39, K.156, N.179 Ligand excluded by PLIP ACT.10: 5 residues within 4Å: Chain A: C.152, V.153, L.154, A.155 Chain D: S.385 Ligand excluded by PLIP ACT.11: 2 residues within 4Å: Chain A: N.195, E.197 Ligand excluded by PLIP ACT.12: 8 residues within 4Å: Chain A: S.388, R.418 Chain D: G.35, H.159, M.160, G.161 Ligands: MPD.5, MPD.6 Ligand excluded by PLIP ACT.13: 10 residues within 4Å: Chain D: H.220, N.319, V.323, P.324, R.327, P.337, M.414, V.415, I.416 Ligands: MPD.6 Ligand excluded by PLIP ACT.14: 1 residues within 4Å: Chain A: E.175 Ligand excluded by PLIP ACT.24: 7 residues within 4Å: Chain A: L.48, R.141, D.146 Chain D: N.310, P.311, V.312 Ligands: MPD.21 Ligand excluded by PLIP ACT.25: 5 residues within 4Å: Chain D: M.19, T.20, P.21, V.22, R.301 Ligand excluded by PLIP ACT.26: 4 residues within 4Å: Chain D: T.25, A.39, K.156, N.179 Ligand excluded by PLIP ACT.27: 5 residues within 4Å: Chain A: S.385 Chain D: C.152, V.153, L.154, A.155 Ligand excluded by PLIP ACT.28: 2 residues within 4Å: Chain D: N.195, E.197 Ligand excluded by PLIP ACT.29: 8 residues within 4Å: Chain A: G.35, H.159, M.160, G.161 Chain D: S.388, R.418 Ligands: MPD.22, MPD.23 Ligand excluded by PLIP ACT.30: 10 residues within 4Å: Chain A: H.220, N.319, V.323, P.324, R.327, P.337, M.414, V.415, I.416 Ligands: MPD.23 Ligand excluded by PLIP ACT.31: 1 residues within 4Å: Chain D: E.175 Ligand excluded by PLIP

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.15: 6 residues within 4Å: Chain A: V.183, S.246, R.247, A.248, D.249, K.302 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.247, A:D.249 Water bridges: A:V.183, A:K.302, A:K.302 Salt bridges: A:K.302 PO4.32: 6 residues within 4Å: Chain D: V.183, S.246, R.247, A.248, D.249, K.302 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.247, D:D.249 Water bridges: D:V.183, D:D.249, D:K.302, D:K.302 Salt bridges: D:K.302

2 x NA: SODIUM ION(Non-functional Binders)

NA.16: 6 residues within 4Å: Chain A: G.287, L.288, P.289, P.308, N.310, S.313 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.287, A:S.313, A:S.313 Water bridges: A:L.288 NA.33: 6 residues within 4Å: Chain D: G.287, L.288, P.289, P.308, N.310, S.313 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.287, D:S.313 Water bridges: D:L.288

2 x 3F8: 1,1'-[ethane-1,2-diylbis(oxyethane-2,1-diyl)]bis(1H-pyrrole-2,5-dione)(Covalent)

3F8.17: 10 residues within 4Å: Chain B: Y.8, P.9, C.10 Chain C: Y.8, P.9, C.10 Chain D: H.365, Q.366, E.367, P.368 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.8 3F8.34: 10 residues within 4Å: Chain A: H.365, Q.366, E.367, P.368 Chain E: Y.8, P.9, C.10 Chain F: Y.8, P.9, C.10 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., Elucidating the Molecular Basis for Inhibitory Neurotransmission Regulation by Artemisinins. Neuron (2019)

Release Date

2019-01-16

Peptides

Gephyrin: AD
Gamma-aminobutyric acid receptor subunit alpha-3: BCEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
D

C
E

E
D

F
E

Gephyrin

Gamma-aminobutyric acid receptor subunit alpha-3

Related Entries With Identical Sequence